The Architecture of Metabolism Maximizes Biosynthetic Diversity in the Largest Class of Fungi

Abstract Ecological diversity in fungi is largely defined by metabolic traits, including the ability to produce secondary or “specialized” metabolites (SMs) that mediate interactions with other organisms. Fungal SM pathways are frequently encoded in biosynthetic gene clusters (BGCs), which facilitate the identification and characterization of metabolic pathways. Variation in BGC composition reflects the diversity of their SM products. Recent studies have documented surprising diversity of BGC repertoires among isolates of the same fungal species, yet little is known about how this population-level variation is inherited across macroevolutionary timescales. Here, we applied a novel linkage-based algorithm to reveal previously unexplored dimensions of diversity in BGC composition, distribution, and repertoire across 101 species of Dothideomycetes, which are considered the most phylogenetically diverse class of fungi and known to produce many SMs. We predicted both complementary and overlapping sets of clustered genes compared with existing methods and identified novel gene pairs that associate with known secondary metabolite genes. We found that variation among sets of BGCs in individual genomes is due to nonoverlapping BGC combinations and that several BGCs have biased ecological distributions, consistent with niche-specific selection. We observed that total BGC diversity scales linearly with increasing repertoire size, suggesting that secondary metabolites have little structural redundancy in individual fungi. We project that there is substantial unsampled BGC diversity across specific families of Dothideomycetes, which will provide a roadmap for future sampling efforts. Our approach and findings lend new insight into how BGC diversity is generated and maintained across an entire fungal taxonomic class.

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The architecture of metabolism maximizes biosynthetic diversity in the largest class of fungi

10.1101/2020.01.31.928846 ◽

2020 ◽

Cited By ~ 1

Author(s):

Emile Gluck-Thaler ◽

Sajeet Haridas ◽

Manfred Binder ◽

Igor V. Grigoriev ◽

Pedro W. Crous ◽

...

Keyword(s):

Population Level ◽

Gene Clusters ◽

Fungal Species ◽

Structural Redundancy ◽

Biosynthetic Gene Clusters ◽

Taxonomic Class ◽

Overlapping Sets ◽

Identification And Characterization ◽

Insight Into

Abstract:BackgroundEcological diversity in fungi is largely defined by metabolic traits, including the ability to produce secondary or “specialized” metabolites (SMs) that mediate interactions with other organisms. Fungal SM pathways are frequently encoded in biosynthetic gene clusters (BGCs), which facilitate the identification and characterization of metabolic pathways. Variation in BGC composition reflects the diversity of their SM products. Recent studies have documented surprising diversity of BGC repertoires among isolates of the same fungal species, yet little is known about how this population-level variation is inherited across macroevolutionary timescales.ResultsHere, we applied a novel linkage-based algorithm to reveal previously unexplored dimensions of diversity in BGC composition, distribution, and repertoire across 101 species of Dothideomycetes, which are considered to be the most phylogenetically diverse class of fungi and are known to produce many SMs. We predicted both complementary and overlapping sets of clustered genes compared with existing methods and identified novel gene pairs that associate with known secondary metabolite genes. We found that variation in BGC repertoires is due to non-overlapping BGC combinations and that several BGCs have biased ecological distributions, consistent with niche-specific selection. We observed that total BGC diversity scales linearly with increasing repertoire size, suggesting that secondary metabolites have little structural redundancy in individual fungi.ConclusionsWe project that there is substantial unsampled BGC diversity across specific families of Dothideomycetes, which will provide a roadmap for future sampling efforts. Our approach and findings lend new insight into how BGC diversity is generated and maintained across an entire fungal taxonomic class.

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Activation and Identification of a Griseusin Cluster in Streptomyces sp. CA-256286 by Employing Transcriptional Regulators and Multi-Omics Methods

Molecules ◽

10.3390/molecules26216580 ◽

2021 ◽

Vol 26 (21) ◽

pp. 6580

Author(s):

Charlotte Beck ◽

Tetiana Gren ◽

Francisco Javier Ortiz-López ◽

Tue Sparholt Jørgensen ◽

Daniel Carretero-Molina ◽

...

Keyword(s):

Biosynthetic Pathway ◽

Genome Mining ◽

Gene Clusters ◽

Transcriptional Regulators ◽

Biosynthetic Gene ◽

Biosynthetic Gene Clusters ◽

Heterologous Host ◽

Streptomyces Sp ◽

Identification And Characterization

Streptomyces are well-known producers of a range of different secondary metabolites, including antibiotics and other bioactive compounds. Recently, it has been demonstrated that “silent” biosynthetic gene clusters (BGCs) can be activated by heterologously expressing transcriptional regulators from other BGCs. Here, we have activated a silent BGC in Streptomyces sp. CA-256286 by overexpression of a set of SARP family transcriptional regulators. The structure of the produced compound was elucidated by NMR and found to be an N-acetyl cysteine adduct of the pyranonaphtoquinone polyketide 3′-O-α-d-forosaminyl-(+)-griseusin A. Employing a combination of multi-omics and metabolic engineering techniques, we identified the responsible BGC. These methods include genome mining, proteomics and transcriptomics analyses, in combination with CRISPR induced gene inactivations and expression of the BGC in a heterologous host strain. This work demonstrates an easy-to-implement workflow of how silent BGCs can be activated, followed by the identification and characterization of the produced compound, the responsible BGC, and hints of its biosynthetic pathway.

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Identification and Characterization of Mycemycin Biosynthetic Gene Clusters in Streptomyces olivaceus FXJ8.012 and Streptomyces sp. FXJ1.235

Marine Drugs ◽

10.3390/md16030098 ◽

2018 ◽

Vol 16 (3) ◽

pp. 98 ◽

Cited By ~ 3

Author(s):

Fangying Song ◽

Ning Liu ◽

Minghao Liu ◽

Yihua Chen ◽

Ying Huang

Keyword(s):

Gene Clusters ◽

Biosynthetic Gene ◽

Biosynthetic Gene Clusters ◽

Streptomyces Sp ◽

Streptomyces Olivaceus ◽

Identification And Characterization

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Identification and Characterization of Biosynthetic Gene Clusters from Halophilic Marine Fungus Eurotium rubrum

10.20944/preprints202002.0388.v1 ◽

2020 ◽

Author(s):

Obul Reddy Bandapali ◽

Frederik Teilfeldt Hansen ◽

Alisha Parveen ◽

Pradeep Phule ◽

Emmagouni Sharath Kumar Goud ◽

...

Keyword(s):

Polyketide Synthase ◽

Gene Clusters ◽

Marine Fungus ◽

Type I ◽

Biosynthetic Gene ◽

Biosynthetic Gene Clusters ◽

Peptide Synthetase ◽

Future Drug ◽

Identification And Characterization

Eurotium rubrum is a halophilic marine ascomycete, which can bear the hypersalinities of the Red Sea and proliferate, while most living entities cannot bear this condition. Recently, a 26.2 Mb assembled genome of this fungus had become available. Marine fungi are fascinating organisms capable of harboring several biosynthetic gene clusters (BGCs), which enables them to produce several natural compounds with antibiotic and anticancerous properties. Understanding the BGCs are critically important for the development of biotechnological applications and the discovery of future drugs. There is no knowledge available on the BGCs of this halophilic marine ascomycete. Herein, we set out to explore and characterize BGCs and the corresponding genes from E. rubrum using bioinformatic methods. We deciphered 36 BGCs in the genome of E. rubrum. These 36 BGCs can be grouped into four non-ribosomal peptide synthetase (NRPS) clusters, eight NRPS-like (NRPSL) BGCs, eight type I polyketide synthase (T1PKS), 11 terpene BGCs including one β-lactone cluster, four hybrid BGCs, and two siderophore BGCs. This study is an example of marine genomics application into potential future drug-like compound discovery.

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Screening of polyketide genes from Brazilian Atlantic Forest soil

Universitas Scientiarum ◽

10.11144/javeriana.sc22-1.sopg ◽

2017 ◽

Vol 22 (1) ◽

pp. 87

Author(s):

Roger David Castillo Arteaga ◽

Simone Ichiwaki ◽

Karen Massini ◽

Leandro Maza-Garrido ◽

Edith Mariela Burbano-Rosero ◽

...

Keyword(s):

Atlantic Forest ◽

Bioactive Compounds ◽

Metagenomic Library ◽

Gene Clusters ◽

Brazilian Atlantic Forest ◽

Biosynthetic Gene Clusters ◽

Promising Alternative ◽

Biotechnological Potential ◽

Insight Into

Soil is a large source of microorganisms with potential to produce bioactive compounds. Since most of them cannot be cultured, metagenomics has become a useful tool in order to evaluate this potential. The aim of this study was to screen biosynthetic polyketide genes (PKS) present in a metagenomic library constructed from a soil sample isolated from the Brazilian Atlantic Forest. The library comprises 5000 clones with DNA inserts between 40 and 50 Kb. The characterization of the biosynthetic gene clusters of these molecules is a promising alternative to elucidate the biotechnological potential of bioactive compounds in microbial communities. The PKS genes were screened using degenerated primers. The positive clones for PKS systems were isolated, and their nucleotide sequences analysed with bioinformatics tools. The screening yielded two positive clones for PKS II genes. Furthermore, variations in the sequences of the PKS II genes from the metagenomic library were observed when compared with sequences of ketosynthases’ databases. With these findings we gain insight into the possible relation between new biosynthetic genes and the production of new secondary metabolites.

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Identification and Characterization of Inorganic Pyrophosphatase and PAP Phosphatase from Thermococcus onnurineus NA1

Journal of Bacteriology ◽

10.1128/jb.01699-08 ◽

2009 ◽

Vol 191 (10) ◽

pp. 3415-3419 ◽

Cited By ~ 4

Author(s):

Hyun Sook Lee ◽

Yun Jae Kim ◽

Jung-Hyun Lee ◽

Sung Gyun Kang

Keyword(s):

Gene Clusters ◽

Inorganic Pyrophosphatase ◽

Thermococcus Onnurineus Na1 ◽

First Report ◽

Activation System ◽

Sulfate Activation ◽

Pyrococcus Abyssi ◽

Identification And Characterization ◽

Hypothetical Genes

ABSTRACT Two hypothetical genes were functionally verified to be a pyrophosphatase and a PAP phosphatase in Thermococcus onnurineus NA1. This is the first report of the pyrophosphatases and the PAP phosphatases being organized in the gene clusters of the sulfate activation system only in T. onnurineus NA1 and “Pyrococcus abyssi.”

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Analysis and characterization of coenzyme B12 biosynthetic gene clusters and improvement of B12 biosynthesis in Pseudomonas denitrificans ATCC 13867

FEMS Microbiology Letters ◽

10.1093/femsle/fny211 ◽

2018 ◽

Vol 365 (21) ◽

Cited By ~ 3

Author(s):

Thuan Phu Nguyen-Vo ◽

Satish Kumar Ainala ◽

Jung-Rae Kim ◽

Sunghoon Park

Keyword(s):

Gene Clusters ◽

Coenzyme B12 ◽

Biosynthetic Gene ◽

Biosynthetic Gene Clusters ◽

Pseudomonas Denitrificans

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Biosynthesis of the uridine-derived nucleoside antibiotic A-94964: identification and characterization of the biosynthetic gene cluster provide insight into the biosynthetic pathway

Organic & Biomolecular Chemistry ◽

10.1039/c8ob02765j ◽

2019 ◽

Vol 17 (3) ◽

pp. 461-466 ◽

Cited By ~ 5

Author(s):

Taro Shiraishi ◽

Makoto Nishiyama ◽

Tomohisa Kuzuyama

Keyword(s):

Gene Cluster ◽

In Silico ◽

Biosynthetic Pathway ◽

Gene Deletion ◽

Biosynthetic Gene Cluster ◽

Biosynthetic Gene ◽

Identification And Characterization ◽

Insight Into

The biosynthetic pathway of the uridine-derived nucleoside antibiotic A-94964 was proposed via in silico analysis coupled with gene deletion experiments.

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Use of Permanent Wall-Deficient Cells as a System for the Discovery of New-to-Nature Metabolites

Microorganisms ◽

10.3390/microorganisms8121897 ◽

2020 ◽

Vol 8 (12) ◽

pp. 1897

Author(s):

Shraddha Shitut ◽

Güniz Özer Bergman ◽

Alexander Kros ◽

Daniel E. Rozen ◽

Dennis Claessen

Keyword(s):

Cell Wall ◽

Secondary Metabolites ◽

Gene Clusters ◽

Chemical Diversity ◽

Biosynthetic Gene Clusters ◽

Microbial Cell Factories ◽

Cell Factories ◽

Genome Recombination ◽

Antibiotic Discovery ◽

Insight Into

Filamentous actinobacteria are widely used as microbial cell factories to produce valuable secondary metabolites, including the vast majority of clinically relevant antimicrobial compounds. Secondary metabolites are typically encoded by large biosynthetic gene clusters, which allow for a modular approach to generating diverse compounds through recombination. Protoplast fusion is a popular method for whole genome recombination that uses fusion of cells that are transiently wall-deficient. This process has been applied for both inter- and intraspecies recombination. An important limiting step in obtaining diverse recombinants from fused protoplasts is regeneration of the cell wall, because this forces the chromosomes from different parental lines to segregate, thereby preventing further recombination. Recently, several labs have gained insight into wall-deficient bacteria that have the ability to proliferate without their cell wall, known as L-forms. Unlike protoplasts, L-forms can stably maintain multiple chromosomes over many division cycles. Fusion of such L-forms would potentially allow cells to express genes from both parental genomes while also extending the time for recombination, both of which can contribute to an increased chemical diversity. Here, we present a perspective on how L-form fusion has the potential to become a platform for novel compound discovery and may thus help to overcome the antibiotic discovery void.

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